Creating and managing protein sequences - BioPharma Finder Software - Creating and managing protein sequences - BioPharma Finder Software - BioPharma Finder Software

BioPharma Finder 5.2 Intact Mass Analysis User Guide
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Ardia Platform > Software > BioPharma Finder Software
Desktop Software > BioPharma Finder Software
Document Type
User Guide
Software version
5.2
  • Intact Mass Analysis
  • Copyright Information
  • About the BioPharma Finder application and user guides
  • New to this version
  • Special notices
  • Access the documentation
  • View the user guides
  • View the glossary
  • Update the help system and user guides
  • Contact us
  • Getting started
  • Local mode
  • Ardia platform connection
  • Register with the Ardia platform
  • Sign in to your Ardia platform account
  • Results from earlier BioPharma Finder software versions
  • Ardia platform management
  • Disconnect from the Ardia platform
  • Lock the application
  • Unlock the application
  • Unlock the application as the last logged-in user
  • Unlock the application when the last logged-in user is not available
  • Data space optimization
  • Optimize disk space
  • Purge all BioPharma Finder files
  • Data backup and recovery
  • Create or restore a database Snapshot
  • Manual database backup
  • Exit the application
  • Common features for different analyses
  • Fragmentation methods
  • Create a new experiment
  • Select raw data files
  • Load raw data files
  • Change the location of a raw data file
  • Delete raw data files
  • Select one or more sequences
  • Select a processing method
  • Import a processing method
  • Export a processing method
  • Select a processing method
  • Delete a processing method
  • Save a processing method
  • View and export the Method Summary on the Save Method page
  • Save a processing method
  • Effects after saving the processing method
  • Use the run queue
  • Manage the run queue (except intact mass analysis)
  • Pause the run queue
  • Resume the paused queue
  • Remove jobs from the run queue
  • Manage the run queue for intact mass analysis
  • Pause the run queue
  • Resume the paused queue
  • Remove jobs from the run queue
  • Queue page parameters
  • Organize experiment results
  • Manage experiment results in the Master List
  • Manage folders and experiment results in the Working List
  • Use a Chromeleon-compatible workbook: Intact
  • Import a workbook
  • Export a workbook
  • Delete a workbook
  • Edit an intact workbook
  • Workbook Manager page parameters
  • Workbook Editor page parameters
  • Using the Sequence Manager
  • Sequence Manager tasks
  • Sequence Manager page parameters
  • Creating and managing protein sequences
  • Create and edit protein sequences
  • Import a FASTA file containing a protein sequence
  • Manually create a new protein sequence
  • Select the experiment category for a sequence
  • Edit the amino acids in an existing protein sequence
  • Amino acid letter codes
  • Assigning modifications to a protein sequence
  • Order of modification assignments
  • Manage disulfide links
  • Assign disulfide links
  • Remove disulfide links
  • Disulfide Link Definitions pane parameters
  • Manage static modifications
  • Assign static modifications
  • Remove static modifications
  • Residue Properties and Modifications dialog box parameters
  • Manage glycosylations
  • Manage variable modifications
  • Assign variable modifications
  • Variable Modifications for Peptide Mapping Analysis/Intact Analysis pane parameters
  • Manage proteoforms
  • Define the modification list for proteoforms
  • Generate and save proteoforms
  • All Possible Proteoforms table
  • Change the default modifications for protein sequences
  • Define default modifications for protein sequences
  • Default sublist of modifications for quick loading
  • Manage custom modifications for protein sequences
  • Add custom modifications
  • Edit custom modifications
  • Delete custom modifications
  • Modification Editor pane parameters
  • Save a protein or peptide sequence
  • Save a protein or peptide sequence under the same name (overwrite)
  • Save a protein or peptide sequence under a new name
  • Protein Sequence Editor parameters
  • Using the Host Cell Protein (HCP) Database Manager
  • Add an HCP database
  • Delete an HCP database
  • Using the Theoretical Protein/Peptide Manager
  • Create or import a protein or peptide sequence
  • Specify digestion parameters
  • Add/edit target m/z parameters
  • Add/edit modifications
  • Save a peptide workbook
  • Results table parameters
  • Creating and managing oligonucleotide sequences
  • Create and edit oligonucleotide sequences
  • Import a FASTA file containing an oligonucleotide sequence
  • Manually create a new oligonucleotide sequence
  • Select the experiment category for a sequence
  • Create a mass-only or formula-only oligonucleotide sequence for intact mass analysis
  • Use the Random Sequence Generator for oligonucleotides
  • Change the default modifications for oligonucleotide sequences
  • Define default modifications for oligonucleotide sequences
  • Default sublist of modifications for quick loading
  • Assign custom building blocks to an oligonucleotide sequence
  • Manage variable modifications
  • Assign variable modifications
  • Assign Variable Modifications pane parameters
  • Manage custom modifications and building blocks for oligonucleotides
  • Add custom modifications
  • Add custom building blocks
  • Edit custom modifications or oligo building blocks
  • Delete custom modifications or oligo building blocks
  • Save an oligonucleotide sequence
  • Save an oligonucleotide sequence under the same name (overwrite)
  • Save an oligonucleotide sequence under a new name
  • Oligonucleotide Sequence Editor parameters
  • Intact mass analysis features
  • Deconvolution algorithms
  • Xtract algorithm
  • ReSpect algorithm
  • Quality score algorithm
  • Best results with the ReSpect algorithm
  • Sliding windows deconvolution
  • Processing modes: Manual vs. Automatic
  • Target sequence matching
  • Extracted ion chromatogram (XIC) generation
  • Abundance traces
  • Drug-to-antibody ratio (DAR) values
  • Spectral comparison
  • Running an intact mass analysis
  • Start a new intact mass analysis experiment: Manual mode
  • Process an experiment in Manual mode
  • Start a new intact mass analysis experiment: Automatic mode
  • Process an experiment on the Queue page (Automatic mode)
  • Batch and multiconsensus result formats
  • Working with an intact mass processing method
  • Create or edit a processing method
  • Default processing methods for intact mass analysis
  • Use the processing method editing wizard to edit parameters
  • Edit the Component Detection page
  • Specify parameters on the Component Detection page
  • Chromatogram Parameters area parameters
  • Source Spectra Method area parameters
  • ReSpect deconvolution parameters
  • Xtract deconvolution parameters
  • Plots on the Component Detection page
  • Component detection page commands
  • Edit the Identification page
  • Sequences for target matching experiments
  • Identification page parameters
  • Identification page tables
  • Edit the Report page
  • Report page parameters
  • Edit the Save Method page
  • Viewing intact mass analysis results
  • Open results
  • Open results from the Queue page
  • Open results from the Load Results page
  • Use real-time optimization (RTO) to reprocess results
  • Reporting page: View a deconvolution report
  • Report sections
  • Sample Information section
  • Chromatogram Parameters section
  • Chromatogram section
  • Main Parameters section
  • Advanced Parameters section
  • Source Spectra Parameters section
  • Sequences Information section
  • Source Spectrum section
  • Deconvoluted Spectrum section
  • ReSpect/Xtract Masses Table section
  • Component Details Tables section
  • Source Spectrum Evidence Plot section
  • Reporting page toolbar
  • Spectra Comparison page: Compare deconvoluted spectra
  • Add or remove deconvoluted spectra to the Library
  • Compare deconvoluted spectra
  • Spectra Comparison page parameters
  • Mirror Plot pane commands
  • Viewing the Process and Review page for intact mass analysis
  • View the Results table
  • Change the reference mass
  • Results table parameters (for single file or batch format experiments)
  • Results table parameters (multiconsensus format experiments)
  • Additional Results table parameters for target sequence matching experiments
  • Export the Results table
  • Save an intact workbook
  • Results table commands
  • View the chromatograms
  • Chromatogram plot types
  • Chromatogram pane commands
  • View the deconvoluted spectra
  • Deconvoluted Spectrum pane commands
  • View the source spectra
  • Source Spectrum pane commands
  • View the matched sequence information
  • Change the matched sequence identification for a component
  • Component Information table parameters
  • Target Match Sequence table parameters
  • View the average drug-to-antibody ratio (DAR) values
  • Average DAR table parameters
  • Component Specific Summary table parameters
  • Average DAR pane commands
  • Process and Review page parameters
  • Process and Review page commands
  • Data conversion from legacy applications
  • Converted sequences
  • Converted processing methods
  • Appendix: Handling errors
  • Database service errors
  • Other errors
  • Appendix: Interactive functions
  • Copy and paste functions
  • Copy all contents in a pane
  • Copy a portion of contents in a pane
  • Organize panes
  • Basic chromatogram functions
  • Basic spectrum functions
  • Basic table functions
  • Sort rows
  • Show or hide columns
  • Filter data in a table
  • Filter data rows
  • Table filter operators
  • Table filter operands
  • Create, save, and apply custom filters
  • Remove filters
  • Save filters to a file
  • Apply saved filters to data
  • Appendix: Glycans
  • N-linked glycans in the Define Modification List window
  • N-linked glycans with a CHO host cell-line type
  • N-linked glycans with a human host cell-line type
  • O-linked glycans
  • References
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